Copy Number
The putative cancer-associated PDGs driven by SCNAs in each cancer type were identified by four criteria: 1) located in a peak region of a significantly recurrent focal SNCA locus estimated by the genomic identification of significant targets in cancer (GISTIC2) algorithm, (q≤0.25); 2) altered with high frequency and large amplitude (G-score ≥0.1); 3) mRNA reliably detected in at least 10% of tumor specimens in the given cancer type (90th percentile of FPKM value ≥1); and 4) mRNA significantly and positively correlated with copy numbers (Pearson P-value less than 0.001).
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| Overall_Gscore | No. of Cancer Types | ||||
| HGNC Symbol | Ensembl Gene ID | Amplification | Deletion | Amplification | Deletion |
| PKD2L1 | ENSG00000107593 | 0.00 | 0.00 | 0 | 0 |
| KAZALD1 | ENSG00000107821 | 0.00 | 0.33 | 0 | 1 |
| FGF8 | ENSG00000107831 | 0.00 | 0.00 | 0 | 0 |
| PITRM1 | ENSG00000107959 | 0.16 | 0.17 | 1 | 1 |
| DKK1 | ENSG00000107984 | 0.00 | 0.00 | 0 | 0 |
| PPIF | ENSG00000108179 | 0.39 | 0.00 | 2 | 0 |
| LGI1 | ENSG00000108231 | 0.00 | 0.00 | 0 | 0 |
| CSF3 | ENSG00000108342 | 0.00 | 0.00 | 0 | 0 |
| WNT3 | ENSG00000108379 | 0.00 | 0.00 | 0 | 0 |
| P2RX1 | ENSG00000108405 | 0.00 | 0.00 | 0 | 0 |
| TRIM16L | ENSG00000108448 | 0.78 | 0.16 | 1 | 1 |
| CBX1 | ENSG00000108468 | 0.00 | 0.15 | 0 | 1 |
| SLC25A11 | ENSG00000108528 | 0.00 | 0.12 | 0 | 1 |
| BLMH | ENSG00000108578 | 0.00 | 0.00 | 0 | 0 |
| CCL7 | ENSG00000108688 | 0.00 | 0.00 | 0 | 0 |
| CCL2 | ENSG00000108691 | 0.00 | 0.00 | 0 | 0 |
| CCL8 | ENSG00000108700 | 0.00 | 0.00 | 0 | 0 |
| CCL1 | ENSG00000108702 | 0.00 | 0.00 | 0 | 0 |
| NAGLU | ENSG00000108784 | 0.00 | 0.34 | 0 | 2 |
| HSD17B1 | ENSG00000108786 | 0.00 | 0.00 | 0 | 0 |
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